Sea Shepherd had said the white-bearded captain would be involved in this season's campaign against Japan's whaling operations and he confirmed in a statement that he was back in charge.

"The deck of the Steve Irwin is again under my feet," Watson said late on Tuesday.

"I have an awesome crew and our ship is on course for Antarctica."

Sea Shepherd, whose vessels harass the Japanese whaling fleet to prevent them from slaughtering whales, had previously said its ships would journey north to head off the harpoonists before they reached Antarctica.

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"Apparently they believed it," Watson said.

"Their coastguard mobilised and they went to a great deal of expense and effort to sneak quietly out of port.